Contacts of the strand formed by residues 166 - 173 (chain C) in PDB entry 5NVN
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 166 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C TYR* 5.3 1.8 - - + +
117C LYS* 2.8 41.0 + - - +
155C MET* 3.8 35.4 - - + -
160C PHE* 4.3 14.6 - - + -
162C VAL* 3.7 18.6 - - + -
163C GLY 4.9 2.4 + - - +
164C GLU 3.3 2.7 - - - +
165C GLU* 1.3 77.8 - - - +
167C CYS* 1.3 62.6 + - - +
168C GLY 3.8 4.5 - - - +
182C ILE* 3.8 23.3 - - + -
183C TRP 3.7 5.2 - - - +
185C LYS* 4.1 2.3 - - - -
196C ILE* 3.7 32.1 - - + -
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Residues in contact with CYS 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C PHE* 3.2 19.4 - - + -
117C LYS* 3.0 30.0 + - - +
120C ILE* 4.0 13.2 - - + +
128C ALA 4.0 2.5 - - - -
129C ASN* 3.2 28.0 - - - +
155C MET* 5.2 0.2 - - - -
166C ILE* 1.3 76.5 - - - +
168C GLY* 1.3 56.6 + - - +
183C TRP* 2.8 16.5 + - + +
184C ASN 3.7 5.6 - - - -
185C LYS* 3.3 46.7 - - - -
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Residues in contact with GLY 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C LEU 2.9 14.4 - - - -
116C PHE* 3.7 13.8 - - - -
117C LYS 4.8 0.2 - - - -
155C MET* 3.8 13.0 - - - -
166C ILE* 3.8 2.2 - - - +
167C CYS* 1.3 83.2 - - - +
169C ALA* 1.3 60.3 + - - -
182C ILE* 3.4 6.2 - - - +
183C TRP 2.8 26.4 + - - -
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Residues in contact with ALA 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C HIS* 3.3 3.1 - - - -
115C LEU 2.7 31.2 + - - -
116C PHE* 3.6 1.4 - - - -
148C TRP* 3.6 12.9 - - + -
151C LEU* 3.7 23.6 - - + -
152C ILE* 4.5 1.3 - - + -
155C MET* 3.8 20.9 - - + -
168C GLY* 1.3 74.3 - - - +
170C VAL* 1.3 66.1 - - - +
181C SER 3.3 12.8 - - - +
182C ILE* 4.7 2.2 - - + -
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Residues in contact with VAL 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C ASP* 4.1 3.4 - - - +
113C PHE 3.3 11.9 - - - +
114C HIS* 3.7 23.6 - - + +
116C PHE* 3.7 19.7 - - + -
148C TRP* 3.5 4.0 - - - -
169C ALA* 1.3 80.7 - - - +
171C VAL* 1.3 64.6 + - - +
172C SER* 3.7 19.3 - - - +
179C ILE 4.0 0.4 - - - +
180C ILE* 3.3 7.8 - - - +
181C SER* 2.9 40.2 + - - +
183C TRP* 3.7 25.4 - - + +
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Residues in contact with VAL 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C PRO* 3.9 27.4 - - + -
107C LEU* 5.8 1.5 - - + +
111C SER 4.1 0.2 - - - +
112C ASP* 3.2 5.2 - - - +
113C PHE* 2.9 49.8 + - + +
144C ALA* 4.0 19.5 - - + +
148C TRP* 3.5 38.3 - - + -
170C VAL* 1.3 74.1 - - - +
172C SER* 1.3 69.6 - - - +
173C VAL* 4.2 3.0 + - + +
179C ILE 3.3 9.4 - - - +
180C ILE* 4.4 6.1 - - + +
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Residues in contact with SER 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C SER 3.6 4.3 - - - -
112C ASP* 3.0 27.1 + - - -
170C VAL* 3.7 9.4 - - - +
171C VAL* 1.3 74.5 - - - +
173C VAL* 1.3 62.7 + - - +
174C ARG* 3.7 16.7 + - - +
178C ASP* 3.3 5.9 - - - +
179C ILE* 2.7 55.5 + - - +
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Residues in contact with VAL 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C PRO* 3.2 38.4 - - + +
105C GLY* 5.0 1.3 - - - -
107C LEU* 3.9 21.5 - - + +
109C GLY 3.1 24.3 - - - +
111C SER* 3.0 31.2 + - - +
141C LYS* 4.6 5.2 - - - +
144C ALA* 5.0 0.4 - - + -
171C VAL* 4.8 3.8 - - + +
172C SER* 1.3 74.4 - - - +
174C ARG* 1.3 77.3 + - - +
178C ASP* 3.2 18.8 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il